def add_file(sbml_path, file_path, file_type):
LOGGER.info("Reading SBML '%s'.", sbml_path)
model = read_sbml_model(sbml_path)
LOGGER.info("Writing {} '{}'.".format(file_type.upper(), file_path))
if file_type == "yaml":
save_yaml_model(model, file_path, sort=True)
# Use subprocess rather than gitpython because gitpython cannot get a lock
# on the git DB and thus raises an exception.
check_output(["git", "add", file_path])
def test_save_yaml_model(tmpdir, mini_model):
jsonschema = pytest.importorskip("jsonschema")
"""Test the writing of YAML model."""
output_file = tmpdir.join("mini.yml")
cio.save_yaml_model(mini_model, output_file.strpath, sort=True)
# validate against schema
yaml = YAML(typ="unsafe")
with open(output_file.strpath, "r") as infile:
yaml_to_dict = yaml.load(infile)
dict_to_json = json.dumps(yaml_to_dict)
loaded = json.loads(dict_to_json)
assert jsonschema.validate(loaded, cio.json.json_schema)
def test_save_yaml_model(tmpdir, mini_model):
jsonschema = pytest.importorskip("jsonschema")
"""Test the writing of YAML model."""
output_file = tmpdir.join("mini.yml")
cio.save_yaml_model(mini_model, output_file.strpath, sort=True)
# validate against schema
yaml = YAML(typ="unsafe")
with open(output_file.strpath, "r") as infile:
yaml_to_dict = yaml.load(infile)
dict_to_json = json.dumps(yaml_to_dict)
loaded = json.loads(dict_to_json)
assert jsonschema.validate(loaded, cio.json.json_schema)
for g in mini.genes:
try:
tg = textbook.genes.get_by_id(g.id)
except KeyError:
continue
g.name = tg.name
g.annotation = tg.annotation
mini.reactions.sort()
mini.genes.sort()
mini.metabolites.sort()
# output to various formats
with open("mini.pickle", "wb") as outfile:
dump(mini, outfile, protocol=2)
save_matlab_model(mini, "mini.mat")
save_json_model(mini, "mini.json", pretty=True)
save_yaml_model(mini, "mini.yml")
write_sbml_model(mini, "mini_fbc2.xml")
write_sbml_model(mini, "mini_fbc2.xml.bz2")
write_sbml_model(mini, "mini_fbc2.xml.gz")
write_sbml_model(mini, "mini_cobra.xml", use_fbc_package=False)
raven = load_matlab_model("raven.mat")
with open("raven.pickle", "wb") as outfile:
dump(raven, outfile, protocol=2)
# TODO:these need a reference solutions rather than circular solution checking!
# fva results
fva_result = cobra.flux_analysis.flux_variability_analysis(textbook)
clean_result = OrderedDict()
for key in sorted(fva_result):
clean_result[key] = {k: round(v, 5) for k, v in fva_result[key].items()}